9RJZ | pdb_00009rjz

W-formate dehydrogenase Q447A from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SDR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.946	α = 90
b = 127.011	β = 90
c = 149.158	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 S 9M		2023-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.123	59.546	91.5	0.985	6.3	6.5		59308

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.123	2.26			0.638

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.123	59.546	59270	2920	84.044	0.215	0.2129	0.2211	0.2609	0.271	33.121

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.205			-0.142		-0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.946
r_dihedral_angle_4_deg	21.305
r_dihedral_angle_3_deg	14.565
r_dihedral_angle_1_deg	7.56
r_lrange_it	3.632
r_lrange_other	3.621
r_mcangle_it	2.224
r_mcangle_other	2.224
r_scangle_it	1.965
r_scangle_other	1.964
r_angle_refined_deg	1.47
r_mcbond_it	1.33
r_mcbond_other	1.33
r_angle_other_deg	1.173
r_scbond_it	1.166
r_scbond_other	1.166
r_nbd_other	0.241
r_nbd_refined	0.194
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.15
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9179
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	183

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
pointless	data scaling